---
pretty_name: Amalgam
license: other
license_name: amalgam-upstream
license_link: LICENSE.md
configs:
  - config_name: cliques
    default: true
    data_files:
      - split: activity
        path: cliques/activity.parquet
      - split: anatomical_entity
        path: cliques/anatomical_entity.parquet
      - split: behavior
        path: cliques/behavior.parquet
      - split: biological_entity
        path: cliques/biological_entity.parquet
      - split: biological_process
        path: cliques/biological_process.parquet
      - split: cell
        path: cliques/cell.parquet
      - split: cell_line
        path: cliques/cell_line.parquet
      - split: cellular_component
        path: cliques/cellular_component.parquet
      - split: chemical_entity
        path: cliques/chemical_entity.parquet
      - split: chemical_mixture
        path: cliques/chemical_mixture.parquet
      - split: clinical_attribute
        path: cliques/clinical_attribute.parquet
      - split: clinical_finding
        path: cliques/clinical_finding.parquet
      - split: clinical_intervention
        path: cliques/clinical_intervention.parquet
      - split: cohort
        path: cliques/cohort.parquet
      - split: complex_molecular_mixture
        path: cliques/complex_molecular_mixture.parquet
      - split: device
        path: cliques/device.parquet
      - split: disease
        path: cliques/disease.parquet
      - split: drug
        path: cliques/drug.parquet
      - split: event
        path: cliques/event.parquet
      - split: food
        path: cliques/food.parquet
      - split: gene
        path: cliques/gene.parquet
      - split: gene_family
        path: cliques/gene_family.parquet
      - split: genomic_entity
        path: cliques/genomic_entity.parquet
      - split: geographic_location
        path: cliques/geographic_location.parquet
      - split: gross_anatomical_structure
        path: cliques/gross_anatomical_structure.parquet
      - split: human
        path: cliques/human.parquet
      - split: information_content_entity
        path: cliques/information_content_entity.parquet
      - split: life_stage
        path: cliques/life_stage.parquet
      - split: macromolecular_complex
        path: cliques/macromolecular_complex.parquet
      - split: molecular_activity
        path: cliques/molecular_activity.parquet
      - split: molecular_entity
        path: cliques/molecular_entity.parquet
      - split: molecular_mixture
        path: cliques/molecular_mixture.parquet
      - split: named_thing
        path: cliques/named_thing.parquet
      - split: nucleic_acid_entity
        path: cliques/nucleic_acid_entity.parquet
      - split: organism_taxon
        path: cliques/organism_taxon.parquet
      - split: pathway
        path: cliques/pathway.parquet
      - split: phenomenon
        path: cliques/phenomenon.parquet
      - split: phenotypic_feature
        path: cliques/phenotypic_feature.parquet
      - split: physical_entity
        path: cliques/physical_entity.parquet
      - split: physiological_process
        path: cliques/physiological_process.parquet
      - split: polypeptide
        path: cliques/polypeptide.parquet
      - split: population_of_individual_organisms
        path: cliques/population_of_individual_organisms.parquet
      - split: posttranslational_modification
        path: cliques/posttranslational_modification.parquet
      - split: procedure
        path: cliques/procedure.parquet
      - split: protein
        path: cliques/protein.parquet
      - split: sequence_variant
        path: cliques/sequence_variant.parquet
      - split: small_molecule
        path: cliques/small_molecule.parquet
      - split: taxonomic_rank
        path: cliques/taxonomic_rank.parquet
  - config_name: crossrefs
    data_files:
      - split: clinvar
        path: crossrefs/clinvar.parquet
      - split: obo_apo
        path: crossrefs/obo_apo.parquet
      - split: obo_fao
        path: crossrefs/obo_fao.parquet
      - split: obo_fbdv
        path: crossrefs/obo_fbdv.parquet
      - split: obo_fypo
        path: crossrefs/obo_fypo.parquet
      - split: obo_hsapdv
        path: crossrefs/obo_hsapdv.parquet
      - split: obo_maxo
        path: crossrefs/obo_maxo.parquet
      - split: obo_mmusdv
        path: crossrefs/obo_mmusdv.parquet
      - split: obo_mp
        path: crossrefs/obo_mp.parquet
      - split: obo_taxrank
        path: crossrefs/obo_taxrank.parquet
      - split: obo_to
        path: crossrefs/obo_to.parquet
      - split: obo_wbls
        path: crossrefs/obo_wbls.parquet
      - split: obo_wbphenotype
        path: crossrefs/obo_wbphenotype.parquet
      - split: obo_zfs
        path: crossrefs/obo_zfs.parquet
      - split: obo_zp
        path: crossrefs/obo_zp.parquet
task_categories:
  - other
tags:
  - biology
  - biomedical
  - entity-linking
  - synonyms
  - biolink
size_categories:
  - 100M<n<1B
---

# Amalgam

Amalgam is a biomedical metaontology: a cross-resource integration layer of entity identifiers, names,
and typed cross-references organized by Biolink class. It integrates source ontologies rather than replacing
their semantics; typed associations are not equivalence assertions.

Biomedical entity names for [Biolink](https://biolink.github.io/biolink-model/) classes, built from
[BABEL](https://github.com/NCATSTranslator/Babel) snapshot `local:/home/sgoetz/babel-snapshots/2026jul22`. Cliques that share a preferred name
within a class and taxon scope may merge unless identifier namespaces conflict. Every synonym is assigned to one CURIE within its
class and taxon scope. Strings are kept as written; normalization is left to consumers.

Additional sources:

- [GTDB](https://gtdb.ecogenomic.org/): `GTDB:` taxa (`organism_taxon`); species carry their NCBI species taxid crossref as a `GTDB:` synonym of the `NCBITaxon:` row (at most one GTDB species per taxid).
- [ClinVar](https://www.ncbi.nlm.nih.gov/clinvar/) `variant_summary`: one `CLINVAR:` row per variation and one `DBSNP:rs...` row per referenced rsID (`sequence_variant`), never merged with each other.
- OBO ontologies not in BABEL (`config/obo_sources.yaml`): active own-prefix terms with names, EXACT synonyms and alt_ids.

## Subsets

### `cliques` (default)

One row per clique, one split per Biolink class.

| column | type | meaning |
|---|---|---|
| `CURIE` | string | clique leader identifier |
| `PREFERRED_NAME` | string | preferred name, as written |
| `CLASS` | string | Biolink class, e.g. `biolink:Gene` (split `gene`) |
| `SYNONYMS` | list<string> | sorted names; may be empty when every name lost arbitration |
| `TAXA` | list<string> | sorted `NCBITaxon:` CURIEs; empty when taxonless |

| split | class | rows |
---|---|---:|
 `activity` | `biolink:Activity` | 9092 |
 `anatomical_entity` | `biolink:AnatomicalEntity` | 149423 |
 `behavior` | `biolink:Behavior` | 4202 |
 `biological_entity` | `biolink:BiologicalEntity` | 110 |
 `biological_process` | `biolink:BiologicalProcess` | 43888 |
 `cell` | `biolink:Cell` | 9096 |
 `cell_line` | `biolink:CellLine` | 38896 |
 `cellular_component` | `biolink:CellularComponent` | 8779 |
 `chemical_entity` | `biolink:ChemicalEntity` | 372988 |
 `chemical_mixture` | `biolink:ChemicalMixture` | 489 |
 `clinical_attribute` | `biolink:ClinicalAttribute` | 112982 |
 `clinical_finding` | `biolink:ClinicalFinding` | 11065 |
 `clinical_intervention` | `biolink:ClinicalIntervention` | 36772 |
 `cohort` | `biolink:Cohort` | 950 |
 `complex_molecular_mixture` | `biolink:ComplexMolecularMixture` | 572 |
 `device` | `biolink:Device` | 73167 |
 `disease` | `biolink:Disease` | 365181 |
 `drug` | `biolink:Drug` | 293866 |
 `event` | `biolink:Event` | 288 |
 `food` | `biolink:Food` | 9108 |
 `gene` | `biolink:Gene` | 2408081 |
 `gene_family` | `biolink:GeneFamily` | 28437 |
 `genomic_entity` | `biolink:GenomicEntity` | 42421 |
 `geographic_location` | `biolink:GeographicLocation` | 4698 |
 `gross_anatomical_structure` | `biolink:GrossAnatomicalStructure` | 12610 |
 `human` | `biolink:Human` | 46 |
 `information_content_entity` | `biolink:InformationContentEntity` | 54550 |
 `life_stage` | `biolink:LifeStage` | 1357 |
 `macromolecular_complex` | `biolink:MacromolecularComplex` | 19843 |
 `molecular_activity` | `biolink:MolecularActivity` | 198929 |
 `molecular_entity` | `biolink:MolecularEntity` | 14 |
 `molecular_mixture` | `biolink:MolecularMixture` | 11625271 |
 `named_thing` | `biolink:NamedThing` | 32 |
 `nucleic_acid_entity` | `biolink:NucleicAcidEntity` | 551 |
 `organism_taxon` | `biolink:OrganismTaxon` | 3141304 |
 `pathway` | `biolink:Pathway` | 53769 |
 `phenomenon` | `biolink:Phenomenon` | 332529 |
 `phenotypic_feature` | `biolink:PhenotypicFeature` | 88485 |
 `physical_entity` | `biolink:PhysicalEntity` | 6624 |
 `physiological_process` | `biolink:PhysiologicalProcess` | 108 |
 `polypeptide` | `biolink:Polypeptide` | 219 |
 `population_of_individual_organisms` | `biolink:PopulationOfIndividualOrganisms` | 13383 |
 `posttranslational_modification` | `biolink:PosttranslationalModification` | 1971 |
 `procedure` | `biolink:Procedure` | 449455 |
 `protein` | `biolink:Protein` | 2344320 |
 `sequence_variant` | `biolink:SequenceVariant` | 7336430 |
 `small_molecule` | `biolink:SmallMolecule` | 111621082 |
 `taxonomic_rank` | `biolink:TaxonomicRank` | 77 |

### `crossrefs`

Typed associations, not equivalence. One split per source; source lives in the split name, not a column.
Edges retain pre-merge IDs and may refer to rows absent from `cliques`. A zero-row `empty` split is emitted
when no source contributes edges. Read that empty split with `streaming=True`; the datasets library
rejects zero-row splits in materialized mode.

 column | type | meaning |
---|---|---|
 `SUBJECT` | string | source CURIE (pre-merge identifier, may be obsolete) |
 `PREDICATE` | string | edge type, below |
 `OBJECT` | string | target CURIE |

 split | source | rows |
---|---|---:|
 `clinvar` | `clinvar` | 7530759 |
 `obo_apo` | `obo:APO` | 9 |
 `obo_fao` | `obo:FAO` | 33 |
 `obo_fbdv` | `obo:FBdv` | 8 |
 `obo_fypo` | `obo:FYPO` | 100 |
 `obo_hsapdv` | `obo:HsapDv` | 225 |
 `obo_maxo` | `obo:MAXO` | 654 |
 `obo_mmusdv` | `obo:MmusDv` | 77 |
 `obo_mp` | `obo:MP` | 749 |
 `obo_taxrank` | `obo:TAXRANK` | 96 |
 `obo_to` | `obo:TO` | 897 |
 `obo_wbls` | `obo:WBls` | 2 |
 `obo_wbphenotype` | `obo:WBPhenotype` | 42 |
 `obo_zfs` | `obo:ZFS` | 90 |
 `obo_zp` | `obo:ZP` | 52 |

- `dbsnp_reference`: ClinVar variation to the dbSNP rsID it references (one rsID can cover several alleles)
- `gene_association`: variant to the NCBIGene it lies in (location, not identity)
- `replaced_by`: obsolete OBO term to its successor
- `xref`: OBO term cross-reference (relevance only, per OBO 1.4)

## Usage

```python
from datasets import load_dataset

genes = load_dataset("SkyeAv/amalgam", "cliques", split="gene")
cliques = load_dataset("SkyeAv/amalgam", "cliques")  # DatasetDict, one entry per class
edges = load_dataset("SkyeAv/amalgam", "crossrefs", split="clinvar")
```

## Construction

- Synonyms are unique per (class, taxon scope); the same string may recur across classes or taxa.
  Ties go to: preferred-name match, most synonyms, most identifiers, curated sources, smallest CURIE.
- Conflated BABEL files are never read; drugs and chemicals, genes and proteins stay distinct.
- A CURIE-like preferred name uses the first sorted, admitted non-CURIE synonym when available.
  Existing human-readable preferred names are preserved.
- `biolink:Publication` and `biolink:Agent` are dropped.
- Except `biolink:OrganismTaxon`, rows with taxa keep at least one of the 100 allowlisted taxa (`config/taxa.yaml`). Taxonless rows first
  inherit the taxon of single-species identifiers (MGI, RGD, ZFIN, FlyBase, WormBase, SGD, HGNC, Ensembl).

- Junk names are removed: numbers, `uncharacterized`, `hypothetical`, `language`, and stopwords
  (`config/filters.yaml`). Leader CURIEs and equivalent identifiers are indexed as synonyms (fullmap parity).

Generated 2026-10-28 by [Amalgam](https://github.com/SkyeAv/Amalgam).

## License

No single license covers this dataset: each name keeps the terms of the resource it came from, and several
(UMLS, OMIM, DrugBank, KEGG, Orphanet, HMDB) restrict redistribution or commercial use. See
[LICENSE.md](LICENSE.md) before use.